Search Results - "Breitwieser, Florian"

Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification by Breitwieser, Florian P, Salzberg, Steven L

“…Abstract Summary Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze,…”
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Centrifuge: rapid and sensitive classification of metagenomic sequences by Kim, Daehwan, Song, Li, Breitwieser, Florian P, Salzberg, Steven L

“…Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop…”
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Metagenome analysis using the Kraken software suite by Lu, Jennifer, Rincon, Natalia, Wood, Derrick E., Breitwieser, Florian P., Pockrandt, Christopher, Langmead, Ben, Salzberg, Steven L., Steinegger, Martin

“…Metagenomic experiments expose the wide range of microscopic organisms in any microbial environment through high-throughput DNA sequencing. The computational…”
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A review of methods and databases for metagenomic classification and assembly by Breitwieser, Florian P, Lu, Jennifer, Salzberg, Steven L

“…Abstract Microbiome research has grown rapidly over the past decade, with a proliferation of new methods that seek to make sense of large, complex data sets…”
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Bracken: estimating species abundance in metagenomics data by Lu, Jennifer, Breitwieser, Florian P, Thielen, Peter, Salzberg, Steven L

“…Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample…”
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Human contamination in bacterial genomes has created thousands of spurious proteins by Breitwieser, Florian P, Pertea, Mihaela, Zimin, Aleksey V, Salzberg, Steven L

“…Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and…”
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CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise by Pertea, Mihaela, Shumate, Alaina, Pertea, Geo, Varabyou, Ales, Breitwieser, Florian P, Chang, Yu-Chi, Madugundu, Anil K, Pandey, Akhilesh, Salzberg, Steven L

“…We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and…”
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Author Correction: Metagenome analysis using the Kraken software suite by Lu, Jennifer, Rincon, Natalia, Wood, Derrick E, Breitwieser, Florian P, Pockrandt, Christopher, Langmead, Ben, Salzberg, Steven L, Steinegger, Martin

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Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebrospinal Fluid Diagnostics by Simner, Patricia J, Miller, Heather B, Breitwieser, Florian P, Pinilla Monsalve, Gabriel, Pardo, Carlos A, Salzberg, Steven L, Sears, Cynthia L, Thomas, David L, Eberhart, Charles G, Carroll, Karen C

“…The purpose of this study was to develop and optimize different processing, extraction, amplification, and sequencing methods for metagenomic next-generation…”
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Statistical analysis of co-occurrence patterns in microbial presence-absence datasets by Mainali, Kumar P, Bewick, Sharon, Thielen, Peter, Mehoke, Thomas, Breitwieser, Florian P, Paudel, Shishir, Adhikari, Arjun, Wolfe, Joshua, Slud, Eric V, Karig, David, Fagan, William F

“…Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared…”
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Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing by Li, Zhigang, Breitwieser, Florian P, Lu, Jennifer, Jun, Albert S, Asnaghi, Laura, Salzberg, Steven L, Eberhart, Charles G

“…We test the ability of next-generation sequencing, combined with computational analysis, to identify a range of organisms causing infectious keratitis. This…”
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The Lipid-Modifying Enzyme SMPDL3B Negatively Regulates Innate Immunity by Heinz, Leonhard X., Baumann, Christoph L., Köberlin, Marielle S., Snijder, Berend, Gawish, Riem, Shui, Guanghou, Sharif, Omar, Aspalter, Irene M., Müller, André C., Kandasamy, Richard K., Breitwieser, Florian P., Pichlmair, Andreas, Bruckner, Manuela, Rebsamen, Manuele, Blüml, Stephan, Karonitsch, Thomas, Fauster, Astrid, Colinge, Jacques, Bennett, Keiryn L., Knapp, Sylvia, Wenk, Markus R., Superti-Furga, Giulio

“…Lipid metabolism and receptor-mediated signaling are highly intertwined processes that cooperate to fulfill cellular functions and safeguard cellular…”
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Germline RBBP6 mutations in familial myeloproliferative neoplasms by Harutyunyan, Ashot S., Giambruno, Roberto, Krendl, Christian, Stukalov, Alexey, Klampfl, Thorsten, Berg, Tiina, Chen, Doris, Milosevic Feenstra, Jelena D., Jäger, Roland, Gisslinger, Bettina, Gisslinger, Heinz, Rumi, Elisa, Passamonti, Francesco, Pietra, Daniela, Müller, André C., Parapatics, Katja, Breitwieser, Florian P., Herrmann, Richard, Colinge, Jacques, Bennett, Keiryn L., Superti-Furga, Giulio, Cazzola, Mario, Hammond, Emma, Kralovics, Robert

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A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN by Mazouzi, Abdelghani, Stukalov, Alexey, Müller, André C., Chen, Doris, Wiedner, Marc, Prochazkova, Jana, Chiang, Shih-Chieh, Schuster, Michael, Breitwieser, Florian P., Pichlmair, Andreas, El-Khamisy, Sherif F., Bock, Christoph, Kralovics, Robert, Colinge, Jacques, Bennett, Keiryn L., Loizou, Joanna I.

“…The cellular response to replication stress requires the DNA-damage-responsive kinase ATM and its cofactor ATMIN; however, the roles of this signaling pathway…”
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Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs by Kandathil, Abraham J, Breitwieser, Florian P, Sachithanandham, Jaiprasath, Robinson, Matthew, Mehta, Shruti H, Timp, Winston, Salzberg, Steven L, Thomas, David L, Balagopal, Ashwin

“…Next-generation metagenomic sequencing (NGMS) has opened new frontiers in microbial discovery but has been clinically characterized in only a few settings. To…”
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General Statistical Modeling of Data from Protein Relative Expression Isobaric Tags by Breitwieser, Florian P, Müller, André, Dayon, Loïc, Köcher, Thomas, Hainard, Alexandre, Pichler, Peter, Schmidt-Erfurth, Ursula, Superti-Furga, Giulio, Sanchez, Jean-Charles, Mechtler, Karl, Bennett, Keiryn L, Colinge, Jacques

“…Quantitative comparison of the protein content of biological samples is a fundamental tool of research. The TMT and iTRAQ isobaric labeling technologies allow…”
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Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms by Yee, Rebecca, Breitwieser, Florian P., Hao, Stephanie, Opene, Belita N.A., Workman, Rachael E., Tamma, Pranita D., Dien-Bard, Jennifer, Timp, Winston, Simner, Patricia J.

“…Antimicrobial resistance (AMR) is a public health threat where efficient surveillance is needed to prevent outbreaks. Existing methods for detection of…”
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Isobar(PTM): a software tool for the quantitative analysis of post-translationally modified proteins by Breitwieser, Florian P, Colinge, Jacques

“…The establishment of extremely powerful proteomics platforms able to map thousands of modification sites, e.g. phosphorylations or acetylations, over entire…”
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Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system by Salzberg, Steven L, Breitwieser, Florian P, Kumar, Anupama, Hao, Haiping, Burger, Peter, Rodriguez, Fausto J, Lim, Michael, Quiñones-Hinojosa, Alfredo, Gallia, Gary L, Tornheim, Jeffrey A, Melia, Michael T, Sears, Cynthia L, Pardo, Carlos A

“…OBJECTIVE:To determine the feasibility of next-generation sequencing (NGS) microbiome approaches in the diagnosis of infectious disorders in brain or spinal…”
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Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML by Winter, Georg E, Rix, Uwe, Carlson, Scott M, Gleixner, Karoline V, Grebien, Florian, Gridling, Manuela, Müller, André C, Breitwieser, Florian P, Bilban, Martin, Colinge, Jacques, Valent, Peter, Bennett, Keiryn L, White, Forest M, Superti-Furga, Giulio

“…A systems-pharmacology approach reveals that the combined off-target activity of two kinase inhibitors that impedes MAPK signaling to decrease expression of…”
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